Crop diversification tends to favor the soil fauna community, soil aggregation, and consequently soil organic carbon (SOC) stock. Understanding the association between these attributes can help in understanding the dynamics of physical protection of soil organic matter. In this context, our study aimed to answer: (1) how does the edaphic macrofauna community and soil carbon and aggregate classes respond to two types of coffee agroforestry systems (coffee with Grevillea robusta and coffee with banana) and how these responses differ from native ecosystem; (2) how and to what extent are soil aggregation regulated by the complex structural interactions of plant residue input, SOC, and the soil faunal community? The work was conducted in the municipality of Planalto, state of Bahia, Brazil. Three systems were evaluated: agroforestry system of Coffee arabica L. with Grevillea robusta (CG); agroforestry system of Coffee arabica with Musa spp. (CB); and native forest (NF). Four plots were delimited in each system, in which dry fractionation of the soil was performed to obtain aggregates of classes >6, 6–4, 4–2 and < 2 mm. The macrofauna was sampled using the Tropical Soil Biology and Fertility Program method. The labile and total carbon of the soil and aggregates were determined and the carbon management indices were calculated. The CG and CB presented a greater amount of larger size aggregates (> 6, 6–4 and 4–2 mm) than the NF. The CB system provided more favorable conditions for the soil macrofauna. Despite this, both coffee agroforestry systems favored the occurrence of Oligochaeta. The CG was more favorable to maintain labile fractions of organic matter than the CB. The edaphic fauna show a close relationship with the formation of carbon aggregates and stabilization which was directly influenced by continuous input of plant residues in diverse coffee growing systems.